unanswered Protein CG dynamics

  • sgeorge
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3 years 7 months ago #8679 by sgeorge
Protein CG dynamics was created by sgeorge
Hi,
I am using martini force field to model a 1200 residue protein. I am comparing 14 residue region of the protein with other homologus protein and mainly interested in rmsd and rmsf values of these region. Also I am interested in the representative structure of the most populated cluster of the whole protein from the trajectory and backmap the structure and use for other modeling purpose. I have few questions regarding my approach

1) Can the clustering approach implemented in the gromacs (Daura et al) used for clustering CG trajectory or other geometrical clustering methods such as k-means is appropriate.

2)can the backmapping procedure be applied to the entire trajectory file or the backmapping procedure should be applied to only the representative structure after cluster analysis.
3)Also want to know about the resolution of backmapped structures.
4)After a normal martini simulation if there is no significant changes in rmsd and Rg and other parameters is there a need to do elastic network dynamics.

I don't have much experience in dealing with martini force field and my question may seem naive. Any help will be much appreciated.

Thanking you
Sgeorge

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